I set the Kreg jig for the thinner material's thickness. I presume that you're using the 5/4 material for the head casing and that the backs of both pieces of casing will be in the same plane. I would make a set of 1/2" blocks to be used temporarily for clamping and alignment purposes. I'd support both ends of the 3/4" material long enough to get an effective joint between the casing and head casing. The blocks would be reusable, and if the casing material is consistent in its thickness, one set of blocks should last for the project. If there's an extension of the head casing past the outsides of the vertical casing as I suspect there is, a simple piece tacked to the outside end of the block to hold the casing at the correct distance from the end of the head casing would work with a slightly different piece tacked to the other end of the block to snug the casing into place while screwing the two casing pieces together. If the back surfaces are not dead nuts on with each other, a quick brush with the RO 90 and some Granat 100 would be appropriate to reduce the blocks as necessary. I don't see a need to do any hand planing. Just a thought...